I've looked into this when deciding what system i wanted for my ipod.
First of all do yourself a pleasure and buy an Ipod, there are a lot more options for ipods than the other brands.
Basically there are four options:
Fm transmitter, you plug this in your ipod and then it transmits on a frequencey you choose. This gives 'poor' sound quality (still good tough) and does not charge the battery.
Using the aux plug on the radio, the aux is basically instead of plugging in the headphones you plug in the speakers off your car through the radio, better sound quality, but no charging of the battery
Most car stereo brands offer a cable wich you can plug in the ipod into the disc changer socket in the back of the radio, this will charge the battery and you control the music directly from the radio, this is the system I use and like it a lot!!
Last option is a mp3 ready radio, wich offcourse charges the ipod but you have to control the music from the radio screen, wich I do not like since when you have thousands of songs it's easier to just select them directly from the Ipod instead of through the radio, this is personal preference offcourse.
If you want to use your existing radio the option with the cable wich goes to the cd changer socket is IMHO the best solution.